Dave Peters (davidrpeters@earthlink.net) wrote:
<I think I probably read that as "all branches" rather than "all trees."
Mistake. What the heck is 'all trees anyway'? All possible trees? I'm
confused.>
Programs like MacClade and PAUP* produce more than one tree for a given
dataset, and the more missing or "unknown" scored data ("-" or "?") and
homoplasy, the more variations in tree structure occur. The program will
put every single taxon at every single possible point in relationship to
all other taxa included in the matrix, and then starts paring down the
trees to preserve only those with the shortests steps to get the WHOLE
thing; the number of trees, which for say 150 characters and 70 taxa can
be around 10,000 trees with a reasonably proportion of 10% missing data,
result in your "all possible trees" under the various methods, including
branch-swapping, maximum likelihood, and so forth, that PAUP* and others
can use to find shortest trees. In the end, you can bootstrap, jackknife,
Adams concensus, or strict concensus your set of trees to find "one" tree
and its relative support values depending on included taxa, coded
characters, missing data, or homoplasy. You can even set the concensus
builder to find all trees at a particular step value up or down from any
other value (say, all your trees have 236 steps, you can see what
variation of trees and even a concensus at 237, 250, etc., steps). Steps
won't change if you look for trees under Delayed or Accelerated
Transformation, since this represents the lowest number of supporting
characters shared by both, then whatever additional characters each
algorithm can find.
This is why I am skeptical of find only one single tree, because even
with only 1% missing data in a 70 taxon, 175 character tree (making 12,250
data fields, 1% of these as missing is going to result in over a 120
"unknown" conditions for the whole, and that WILL influence the tree
structure with every variation the program attempts to find for all taxa).
Cheers,
=====
Jaime A. Headden
Little steps are often the hardest to take. We are too used to making leaps
in the face of adversity, that a simple skip is so hard to do. We should all
learn to walk soft, walk small, see the world around us rather than zoom by it.
"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)
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